Helpers Community Inc., a long-standing San Francisco charity, is in big trouble.

After a Chronicle investigation into the charity’s payments and practices, the assessor-recorder’s office is insisting Helpers repay about $31,000 in back taxes after determining it received tax exemptions by misrepresenting its use of four properties it owns.

Experts believe the assessor’s action should invite scrutiny from the state attorney general’s office and the Internal Revenue Service — the two major entities with the power to determine Helpers’ status as a tax-exempt nonprofit.

Helpers Community Inc. has responded to the scrutiny by promising better practices, including the revision of its bylaws to exclude embattled Executive Director Joy Venturini Bianchi from the board. But even that may not be enough to satisfy important regulations about charitable business practices.

Helpers’ sad story has important lessons for the Bay Area’s philanthropists. There are also lessons for members of the public who simply wish to donate money for a good cause.

For philanthropists, the importance of transparency and accountability can’t be understated. Board members must be chosen for their expertise. Executive salaries must stand up to public scrutiny — because they will, eventually, be scrutinized.

Members of the public, meanwhile, should follow the principle of “buyer beware.” It’s easier for smaller charities to fly under regulators’ radar — which means it’s even more necessary for individuals to do their own due diligence before handing over their hard-earned money.